IIRC they were upset she cut her hair short.
I looked up the story and here's an interview with Licia Naff, who played Sonya Gomez.
Cutting and pasting the relevant parts...
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Gomez seemed primed to be a recurring character and a love interest for Geordi, but it ended up being just the two episodes. What happened?
I was told that Gomez was going to evolve into Geordi's love interest, but the dialogue and the way I was directed to play the part was more comic relief than love interest. When it came time to possibly renew me as a recurring role in the next season, I was told that producers thought Gomez was too funny to be the type of love interest that would cause Geordi to get a possibly fatal operation to see me. That was the endgame. Geordi was to fall so deeply in love with me that he'd risk his life to have eye surgery in order to see me. Apparently, the character of Gomez was written comically and didn't match what they really wanted in the end. I was super-bummed when I got the news.
Please share the story about you cutting your hair…
After I shot the two episodes and was told that I was NOT coming back next season, I told the producers “Thank you for the opportunity” and that I was planning to cut my hair length by a few inches, which I did. Little did I know that a few weeks later, the producers wanted me back for a re-shoot of the hallway scene. At that point, they saw my hair didn't match earlier shots and we had to scramble to add extensions to match the previous length. I'm surprised anyone knows that. If I was told to not cut my hair, I never would have, but I'd been completely wrapped from the part with no hope of returning.
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So it looks like they didn't fire her because she cut her hair. They already decided not to continue the character for the third season and told her she wouldn't be coming back. So she cut a few inches off, and then found out they had to do pick-up shots for one of the episodes she was in, and they couldn't because her hair didn't match anymore... and they couldn't be bothered to get hair extensions for her.